Waking Up
by FalconPrincess
Summary: Takes place after STID. The torpedoes are still on the Enterprise, with all their residents sound asleep. A malfunction in one of them causes a young woman to wake up. When Katya tries to escape, she is taken to Kirk. They instantly hate each other, but she is drawn to the Enterprise. What happens when she is placed under Kirk's command? What dark secret is she hiding?
1. Waking Up

When I woke, it was dark, it was cold, and I was scared. I reached out my arms and felt cold metal. I reached up and felt glass. I pushed on it, hard, and it lifted. A rush of warmth came to greet me and I sat up, swinging my legs out of whatever I was in. I pressed my bare feet on the cool floor and tried to stand. I swayed and had to sit back before I attempted again. This time I was successful, and once I was up, I was walking, and then I was running.

I tripped on many things in the dark, but I didn't care what they were; all I cared about was getting out of here. I found my way to a hall and ran to the end, where the door was closed. I smacked my palm around the frame and it slid open. I was momentarily blinded at the light that flooded in from the other room, but I still ran. Once my eyes adjusted I noticed flashed of red all around me. A voice yelled at me to stop, and once I did, I was surrounded.

Men and women in red uniforms with guns looked at me with wide eyes. The grated metal I was standing on pressed into my feet. I nodded to the man who yelled at me and he led me through the ship.

* * *

Hey there! It's me! I just had a kind of cool idea for a story after watching STID and had to get it out. Sorry if this chapter sucks, I was half asleep when I wrote this, but I promise it'll get better! Thanks for reading and please review! And wow this chapter is extremely short. The chapters will get longer too, I promise. Thanks again! :D ~Kendall


	2. The Captain and the Containers

The man led me into a large room full of beeping computers and bustling people. The room was bright and felt unnaturally clean, enough to make me feel ridiculously out of place, and there was a large chair in the center. A young sandy haired man lounged in the chair, his legs draping over one of the arms, eating an apple.

"Captain, we found her running around in the engine room." My captor announced.

The young captain jumped at the sudden loud noise, and everyone in the room stopped what they were doing and turned to stare at me. Not all of them were human; some had green skin and reptilian eyes or slanted eyebrows and pointy ears, but all had the same shocked expression on their face. The captain stood slowly and looked me over, probably trying to figure out how dangerous I was. _Little did he know…_

"What's your name?" the captain asked lazily.

"It's none of your business, that's what it is." I spat. This captain didn't seem like much of a captain. He seemed too arrogant, too naïve to run a ship effectively.

He narrowed his eyes, "As captain of this starship, I order you to tell me your name."

"What ship is this?"

"Stop changing the subject. What's your name?" he was becoming frustrated.

A young man spoke up, "Jim, there seems to be no record of her in any of our systems. Is there a chance that-"

"No, Bones. She's not one of them. She can't be." The captain moved closer, examining me more closely. "Who are you?" he annunciated each word slowly and with precision.

"Is this not the SS Botany Bay?" I looked around the control room, "If so, it's changed quite a bit since I last saw it."

"The Botany Bay? This is the USS Enterprise, and I'm her captain, Jim Kirk. Will you please just answer my damn question?"

I stood still and felt the blood drain from my face. "Jim, you heard her. You heard where she's from, she has to be one of them." The man called Bones said, sounding stressed.

"Bones! Shut up!" Kirk yelled, and then more calmly turned to me. "Do you know what year it is?"

I shook my head. "Can you take me to where I was? Before I escaped?"

Kirk seemed to contemplate it for a short moment, "On one condition: you tell me your name."

I sighed and rolled my eyes. "My name is Katya. I was one of the group of genetically modified humans back in the 90's. Now take me away, _Captain._"

The captain paled. "Right this way." He led me through the ship, and I tried to memorize the layout, but this was much bigger than any ship I had ever seen before, so I gave up on it. We came to a large metal door, Kirk punched in a code, and it slid open, revealing rows upon rows of metal containers. As the lights flickered on, small blue ones in the containers clicked on too. When I padded to the nearest one and looked in the small glass opening on the top, my breath caught in my throat.

A man lay frozen in it. His skin had a blue tint to it and his eyes were closed.

"I know this man. We were both in the same experimental group. Does that mean…?" As the realization sunk in, I ran around, looking in the face of each and every one of my friends and, in some cases, relatives. When I found who I was searching for I dropped to my knees in horror and disbelief. It was Khan in the tube. My husband Khan, the father of my unborn child. I jumped, shocked. I had forgotten all about the baby. I looked to my stomach and wondered if the child would be fine, then rose and placed my hand on the frosted glass above Khan's face.

"You found Khan I see. He was awake not more than two months ago, and caused a hell of a fuss. You just missed him." Bones said, looking at me with concerned eyes. I should have felt anger, anger because I didn't see him, but I just kept staring at his face, holding back my tears.

"You happy now?" Kirk's voice echoed through the room.

I turned to glare at him, "If you're so eager to go then by all means, lead me to a place where I might have a bit of privacy." Everyone filed out, but I hung back for a moment. Before I left, I placed a kiss on the glass just above Khan's lips. I started towards the door, and then noticed Bones looking at me strangely. My pace quickened and I followed Kirk to my room.

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Hi again! Once again, sorry for the short chapter. I don't know why I'm making them so short; I'm usually having to apologize for how long they are, but I can guarantee that as I get more comfortable with writing this they chapters will get longer. Thanks for the reviews and I love you! ~Kendall :D


	3. The Doctor and the Baby

The room was basic but comfortable, with a small bed, a nightstand, a television, and a door that led to a bathroom. Kirk left me at my door with a sour look on his face, almost as if he was thinking about marooning me on the nearest and most dangerous planet. I noticed Bones hanging back once again as I entered my room, but I let my door slide shut before he could say anything.

I sat on the edge of the bed and examined myself. I was wearing the same thing I was when our group was put into the suspended animation tubes; gray-brown capris that showed off my extremely pale calves and feet and a tank top that did the same for my pale arms and chest. I had cropped my pin-straight hair short before we had been frozen, but it had grown so that all down to my waist was covered with thick, dirty blonde hair. I rubbed my eyes tiredly and lay down to try and sleep. Right as I was drifting off, I felt a sick churning in my stomach. My mouth began to water and I rushed to the bathroom.

I don't know how long it was or how many times I had thrown up before someone came to me, but I felt a hand pull back my hair and another rub my back as I knelt over the toilet. When my body had decided it was done, I sat back against the wall, breathing heavily. A cup of water was thrust into my shaking hands and I downed it in a gulp. More water was forced into me until my breathing slowed and my vision cleared, allowing me to recognize the face of my savior. Bones smiled and helped me stand, my arm slung around his neck.

"We need to get you to the Med Bay. Can you walk?"

I nodded and then swung my face in his direction. "Bones I have to tell you something…"

"Yeah I know, you're pregnant. No new information here." I was too out of breath and too tired to ask him how he knew, so I just hobbled along with him to the Med Bay, where he ran what seemed like millions of tests and examinations on every part of me except what I felt really mattered. When he went to scan my brain for the sixteenth time, I grabbed his hand and yanked it away. He looked shocked and reached for a sedative, but I glared at him and his hands fell to his sides.

"Bones, the baby. I need to know if the baby is… if the baby is alive."

He nodded his head and reached for something that I guessed to be an ultrasound and ordered me to pull my shirt up enough to see my stomach. I remembered the ultrasound my mother got when she was pregnant with my sister, when they spread gel across her swollen belly and saw the baby on a snowy gray screen. This was nothing like that. Bones ran a scanner across my stomach and punched a few numbers in, then turned to face me. I prepared myself for the worst, then prompted "Well?"

"You have a very healthy baby growing, Katya. You're about four months along and the baby seems to have nothing wrong with it. Congratulations." Bones said with a smile.

Relief flooded through me and I hugged him. I felt like crying, but I held the tears back and laughed instead. Bones helped me back to my room and decided he would sit in with me until I fell asleep in case I felt sick again. The lights clicked off as I lay down and the room was silent except for the sound of our breathing.

"Bones?" I called out at one point.

"Hmm?" he asked groggily from the chair at my bedside.

"Thanks."

"Yep." The room grew quiet again.

"Oh, and Bones?"

"Yes, Katya." He asked, sounding a bit frustrated.

"It would be awesome if you didn't tell Kirk about the baby. Or anyone for that matter."

"Sure thing. Goodnight." He mumbled.

"Night."

* * *

The next day I was introduced to some of the crew members. Bones had forced me to stay by his side just in case, so I had the opportunity to listen in on all of the problems the Enterprise had and all of the genius ways some people proposed to fix them. I met Lieutenant Uhura when we encountered a crew member who had stopped speaking English after some freak accident in the Cargo Bay. She was kind to me, but hesitant to talk at first. She almost seemed like she didn't know what to do with me, which seemed to be everyone's feeling about me, but she warmed up quickly. We had conversations that switched through almost every language I had learned, then she introduced me to her Vulcan boyfriend, Spock.

Spock didn't take any time at all to warm up to me. He was surprisingly kind right from the start and, like all Vulcans, extremely smart. I found his intelligence quite enlightening and was sad when he and Uhura had to leave. I met Scotty and Chekov at the same time, which was pretty interesting. An injury in the engine room brought Scotty running to us with Chekov chasing after him, apparently bringing news that another had been hurt. Bones took down what had happened, and then ordered the two to stay with me. A beep sounded from the pocket of Chekov's pants and he pulled out his communicator. He tapped on my shoulder, gestured for me to follow him, and walked away.

The twisting passages of the Enterprise were becoming slightly more familiar to me, enough so that I knew we were heading for the Control Room. When the door opened, Kirk whipped around to glare at me.

"Keptin Kork, I brought ze girl." Chekov announced unnecessarily, stepping to the side so everyone could get a better look at me. Kirk charged me, pushing me against the wall and laying his arm across my throat.

"Who woke you up? How the hell did you wake up? Were there any others that were awake?" his breath smelled faintly of alcohol as he spewed the words into my face.

"I don't know. What the hell's the matter with you?" I yelled back.

He screamed in frustration and pushed away from me. "There was an accident in the engine room today, except it wasn't an accident. Someone tried to sabotage our warp core and killed three crew members in the process. I don't suppose you know anything about that either." He spat.

"No, I don't in fact. Try asking some of the people who were actually down there.

He was back in my face in an instant. "How do I know _you_ weren't?"

"Because she was with me all day." Bones announced from the door.

Kirk turned to glare at him, still dangerously close to me. "Why was she with you?"

I shot a warning glance to Bones, who looked apologetic before turning to Kirk. "Because she's four months pregnant, Jim, she needs medical attention."

Kirk faced me, looking confused. "How could she be-"

"She was pregnant before she was frozen. Now let her go before you hurt her."

Kirk backed off, still looking extremely confused, and I ran away to my room. I didn't open the door for anyone but the person bringing me food, not even Bones. I was too angry at him that I feared for his safety should he get too close to me. I spent the next few days alone, trying not to give Kirk a reason to confront me, and for the most part I was successful.

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Hey there! How's it going? This is more like my normal chapter size, and I think I'm liking where this one is going! For those of you asking if there's going to be a pairing, there will be, but not for a little while, and I think it might shock you, which is all I'm gonna say :) anyway, I've had sun poisoning for the past couple days, so I haven't been able to do much, but I'm feeling much better which is awesome! Thanks for the reviews and ciao :) ~Kendall


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